Filtered with samtools flag 1804 (samtools view -F 1804):
read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)
Fraction of mitochondrial reads (unfiltered BAM)
rep1
rep2
Rn = Number of Non-mitochondrial Reads
134092785
134669768
Rm = Number of Mitochondrial Reads
807975
748982
Rm/(Rn+Rm) = Frac. of mitochondrial reads
0.0059894028766035124
0.005530858909862925
SAMstat (filtered/deduped BAM)
rep1
rep2
Total Reads
109277812
109525878
Total Reads (QC-failed)
0
0
Duplicate Reads
0
0
Duplicate Reads (QC-failed)
0
0
Mapped Reads
109277812
109525878
Mapped Reads (QC-failed)
0
0
% Mapped Reads
100.0
100.0
Paired Reads
109277812
109525878
Paired Reads (QC-failed)
0
0
Read1
54638906
54762939
Read1 (QC-failed)
0
0
Read2
54638906
54762939
Read2 (QC-failed)
0
0
Properly Paired Reads
109277812
109525878
Properly Paired Reads (QC-failed)
0
0
% Properly Paired Reads
100.0
100.0
With itself
109277812
109525878
With itself (QC-failed)
0
0
Singletons
0
0
Singletons (QC-failed)
0
0
% Singleton
0.0
0.0
Diff. Chroms
0
0
Diff. Chroms (QC-failed)
0
0
Filtered and duplicates are removed.
Subsampling with atac.subsample_reads is not done in alignment steps.
Nodup BAM is converted into a BED type (TAGALIGN) later and then TAGALIGN is subsampled
with such parameter in the peak-calling step.
Fragment length statistics (filtered/deduped BAM)
rep1
rep2
Fraction of reads in NFR
0.3390878900296575
0.41301047624114595
Fraction of reads in NFR (QC pass)
False
True
Fraction of reads in NFR (QC reason)
out of range [0.4, inf]
OK
NFR / mono-nuc reads
0.5574878496313785
0.7639725034037768
NFR / mono-nuc reads (QC pass)
False
False
NFR / mono-nuc reads (QC reason)
out of range [2.5, inf]
out of range [2.5, inf]
Presence of NFR peak
True
True
Presence of Mono-Nuc peak
True
True
Presence of Di-Nuc peak
True
True
rep1rep2
Open chromatin assays show distinct fragment length enrichments, as the cut
sites are only in open chromatin and not in nucleosomes. As such, peaks
representing different n-nucleosomal (ex mono-nucleosomal, di-nucleosomal)
fragment lengths will arise. Good libraries will show these peaks in a
fragment length distribution and will show specific peak ratios.
NFR: Nucleosome free region
Sequence quality metrics (filtered/deduped BAM)
rep1rep2
Open chromatin assays are known to have significant GC bias. Please take this
into consideration as necessary.
Annotated genomic region enrichment
rep1
rep2
Fraction of Reads in universal DHS regions
0.4295542081314732
0.4208899562530784
Fraction of Reads in blacklist regions
0.003598223580830846
0.0034514948147687983
Fraction of Reads in promoter regions
0.07073438659258661
0.06644051737252452
Fraction of Reads in enhancer regions
0.35549647535036666
0.3512251323837824
Signal to noise can be assessed by considering whether reads are falling into
known open regions (such as DHS regions) or not. A high fraction of reads
should fall into the universal (across cell type) DHS set. A small fraction
should fall into the blacklist regions. A high set (though not all) should
fall into the promoter regions. A high set (though not all) should fall into
the enhancer regions. The promoter regions should not take up all reads, as
it is known that there is a bias for promoters in open chromatin assays.
Library complexity quality metrics
Library complexity (filtered non-mito BAM)
rep1
rep2
Total Fragments
58447808
58074103
Distinct Fragments
54700569
54824302
Positions with Two Read
2902365
2513223
NRF = Distinct/Total
0.935887
0.94404
PBC1 = OneRead/Distinct
0.942972
0.950882
PBC2 = OneRead/TwoRead
17.772091
20.742868
Mitochondrial reads are filtered out by default.
The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads
in a dataset; it is the ratio between the number of positions in the genome
that uniquely mapped reads map to and the total number of uniquely mappable
reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations
with EXACTLY one read pair over the genomic locations with AT LEAST one read
pair. PBC1 is the primary measure, and the PBC1 should be close to 1.
Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking,
0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is
the ratio of genomic locations with EXACTLY one read pair over the genomic
locations with EXACTLY two read pairs. The PBC2 should be significantly
greater than 1.
Fragment: read for a single-ended dataset, pair of reads for a paired-ended dataset
NRF: non redundant fraction
PBC1: PCR Bottleneck coefficient 1
PBC2: PCR Bottleneck coefficient 2
PBC1 is the primary measure. Provisionally
N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2)
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'
Number of raw peaks
rep1
rep2
Number of peaks
264873
258482
The number of peaks is capped at 300000 Peaks are called from macs2 with p-val threshold 0.01
Peak calling statistics
Peak region size
rep1
rep2
idr_opt
overlap_opt
Min size
150.0
150.0
150.0
150.0
25 percentile
224.0
210.0
454.0
375.0
50 percentile (median)
350.0
324.0
691.0
566.0
75 percentile
624.0
582.0
1016.0
875.0
Max size
3322.0
2554.0
3471.0
3471.0
Mean
479.5627678170293
450.2582384846914
775.3431988152536
669.8014403186035
rep1rep2idr_optoverlap_opt
Enrichment / Signal-to-noise ratio
TSS enrichment (filtered/deduped BAM)
rep1
rep2
TSS enrichment
7.692382151686117
7.354598361825624
rep1rep2
Open chromatin assays should show enrichment in open chromatin sites, such as
TSS's. An average TSS enrichment in human (hg19) is above 6. A strong TSS enrichment is
above 10. For other references please see https://www.encodeproject.org/atac-seq/
Jensen-Shannon distance (filtered/deduped BAM)
rep1
rep2
AUC
0.26416786377332707
0.27191882248032284
Synthetic AUC
0.49546711027448853
0.49546942218720447
X-intercept
0.09841671032477635
0.09805478126287248
Synthetic X-intercept
0.0
0.0
Elbow Point
0.6291026958716092
0.6162232202488312
Synthetic Elbow Point
0.50623095733528
0.506253689441241
Synthetic JS Distance
0.3184199050659078
0.3046303531126913
Peak enrichment
Fraction of reads in peaks (FRiP)
FRiP for macs2 raw peaks
rep1
rep2
rep1-pr1
rep2-pr1
rep1-pr2
rep2-pr2
pooled
pooled-pr1
pooled-pr2
Fraction of Reads in Peaks
0.18865671468605172
0.1734038324714457
0.17115146851585938
0.15774441620555799
0.171099564109135
0.15723451506564531
0.19181610694042683
0.1815989741160309
0.1817044418373789
FRiP for overlap peaks
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks
0.16278012039010858
0.15235090907566853
0.13647040565153012
0.16303710417315173
FRiP for IDR peaks
rep1_vs_rep2
rep1-pr1_vs_rep1-pr2
rep2-pr1_vs_rep2-pr2
pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks
0.13961006781924015
0.12725294133817394
0.11198888540295472
0.14051592091522772
For macs2 raw peaks:
repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)
For overlap/IDR peaks:
repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates